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Crystal structure of MINDY1 mutant-Y114F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M Tris-HCl pH 8.5, 1.5 M Ammonium phosphate dibasic
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.16 α = 90 b = 102.16 β = 90 c = 162.714 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2018-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.28 72.24 100 0.282 0.288 0.055 0.998 11.5 27.3 13867
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.28 3.54 99.8 1.765 1.799 0.343 0.902 27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5JKN 3.28 72.21 13097 705 99.86 0.2071 0.205 0.2236 0.2462 0.261 RANDOM 83.772
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 4.15 4.15 -8.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.735 r_dihedral_angle_4_deg 23.612 r_dihedral_angle_3_deg 22.958 r_dihedral_angle_1_deg 10.72 r_angle_refined_deg 2.04 r_angle_other_deg 1.329 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.735 r_dihedral_angle_4_deg 23.612 r_dihedral_angle_3_deg 22.958 r_dihedral_angle_1_deg 10.72 r_angle_refined_deg 2.04 r_angle_other_deg 1.329 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1984 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction